6RXI
In-flow serial synchrotron crystallography using a 3D-printed microfluidic device (3D-MiXD): Lysozyme
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 3 | 293 | 30 mg/mL lysozyme in 100 mM NaAc (pH3.0) rapidly mixed in a 1:1 ratio with precipitant (100 mM NaAc pH 3.0, 20% NaCl, 6% PEG 6000) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.14 | 42.65 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 79.7 | α = 90 |
b = 79.7 | β = 90 |
c = 38.55 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 293 | PIXEL | DECTRIS EIGER X 4M | 2018-02-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE MASSIF-3 | 0.9686 | ESRF | MASSIF-3 |
Serial Crystallography
Sample delivery method | ||
---|---|---|
Diffraction ID | Description | Sample Delivery Method |
1 | injection |
Injection | |||||||
---|---|---|---|---|---|---|---|
Diffraction ID | Description | Flow Rate | Injector Diameter | Injection Power | Injector Nozzle | Filter Size | Carrier Solvent |
1 | 3D-printed microfluidic device | 0.83 | crystallization buffer |
Measurement | |||||
---|---|---|---|---|---|
Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
1 |
Data Reduction | |||
---|---|---|---|
Diffraction ID | Frames Indexed | Crystal Hits | Total Frames |
1 | 450000 | 1000000 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Split (All) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1 | 2 | 56.36 | 100 | 0.06 | 6.21 | 625 | 8876 | 31.3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2 | 2.08 | 100 | 0.57 | 1.83 | 448 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 6H79 | 2 | 56.36 | 8437 | 404 | 99.98 | 0.15984 | 0.15781 | 0.20117 | RANDOM | 36.959 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.38 | -0.38 | 0.75 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.477 |
r_dihedral_angle_4_deg | 24.45 |
r_dihedral_angle_3_deg | 15.726 |
r_long_range_B_other | 7.774 |
r_long_range_B_refined | 7.771 |
r_dihedral_angle_1_deg | 6.827 |
r_scangle_other | 6.373 |
r_scbond_it | 4.179 |
r_scbond_other | 4.175 |
r_mcangle_other | 3.663 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1001 |
Nucleic Acid Atoms | |
Solvent Atoms | 49 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CrystFEL | data reduction |
CrystFEL | data scaling |
MOLREP | phasing |